The Secret of the ARK
by Nitro321
Summary: While fighting an old foe on the Space Colony ARK, Shadow the Hedgehog discovers a secret about his former home, something he would never believe. Now, Shadow and Co. must discover the truth about the ARK, and to stop the threat that can...and will...result from it. Rated T for violence, language, depictions of war, and character death.
1. Prologue

_**Prologue: The Story of Shadow**_

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><p><strong>AN: Hey guys! This is Nitro321, giving you another fanfic! :D**

**So before you say anything: Yes, I have other fanfics going on, and I'm still updating them. This will not effect those stories. But I had this idea, and I couldn't wait to use it, so here it is!**

**The prologue, as it says, is the history of Shadow. This is mainly for those who don't know about Shadow, or for those who want some refreshment on his history. If you don't know much about Shadow, or if you want to learn more about him, then I highly recommend that you read the prologue.**

**But enough jibberish. Enjoy the prologue!**

**I do not own Shadow the Hedgehog, Maria Robotnik, or any of the characters in here! All rights go to SEGA and Sonic Team!**

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><p>Over 50 years ago, the United Federation's government began an experiment to unlock the secrets of immortality. This experiment, code-named Project Shadow, was to take place on the Space Colony ARK, and was to be headed by one of the world's most well-known geniuses at the time: Professor Gerald Robotnik.<p>

The project took several years of hard labor and failed attempts. But it was finally completed. The project was a success, and the world's Ultimate Life Form: named Shadow the Hedgehog, was created.

Professor Robotnik not only had political reasons to create Shadow, but also personal reasons. His granddaughter Maria was ill with a deadly disease, and Shadow was created to help find a cure for the girl.

Shadow and Maria became close friends. So close that they began to see each other as family. They did almost everything together, from exploring the huge space colony to staring out the window at Earth.

A couple months after Shadow was created, another experiment that Professor Robotnik was working on went terribly wrong. The experiment backfired, and before anyone knew it there were demonic creatures all over the space colony, killing who they pleased. Shadow was able to not only destroy the creatures, but was able to use his Chaos powers to heal those who had been injured during the attack.

That incident made Shadow and Maria's friendship grow even more, and the scientists onboard the ARK soon saw that nothing would separate their friendship. They thought it would last forever.

Unfortunately that was not to be the case. The Government Unit of Nations, also known as G.U.N., deemed Shadow too dangerous, and ordered Professor Robotnik to shut him down.

Professor Robotnik, seeing Shadow's power, as well as seeing his ever-growing friendship with his granddaughter, boldly refused, and shut off all communications with G.U.N.

G.U.N., enraged at the Professor's refusal, sent troops to the Space Colony ARK to forcibly shut down Shadow, and to capture the Professor and anyone else who worked on Project Shadow.

On that fatal day, G.U.N. agents burst onto the ARK, and captured the scientists. Maria, who was going into the lab to grab something for her grandfather, saw the G.U.N. agents and quickly ran, provoking one agent to follow her. She ran as fast as she could to Shadow, who understood immediately what was happening. Shadow grabbed Maria's hand and ran as fast as he could toward the escape pods, hoping to escape to Earth with Maria.

The duo reached the escape pods despite the growing number of G.U.N. agents chasing them. Shadow quickly closed and locked the door, hoping to buy time to escape with Maria. Maria however, knew that she was unable to go to Earth, and so put Shadow into a space pod, just as the door was forced open.

The G.U.N. agent aimed his rifle at Maria and ordered her to move. Maria refused, prompting the soldier to shoot her in the chest. With her dying breath Maria asked Shadow to be the protector of the Earth. She asked him to give everyone a chance to be happy. Then, with all the energy she could muster, she pulled the lever, jettisoning the escape pod with Shadow in it.

Fueled with rage and hatred at the sight of Maria's murder, Shadow swore that he would avenge her death by destroying all mankind. However, before he could fulfill that he was captured by G.U.N., who quickly put him in a state of suspended animation for over 50 years.

Fifty years later, Shadow was released from his state of suspended animation by Professor Robotnik's grandson, Dr. Ivo Robotnik, also known as Dr. Eggman. To show his gratitude for releasing him, Shadow agreed to help Dr. Eggman take over the world.

Shadow, Eggman, and undercover agent Rouge the Bat worked together to get the Chaos Emeralds to power up the Eclipse Cannon, a weapon so powerful that it could destroy a whole planet.

Shadow runs into the world-renowned hero Sonic the Hedgehog, and after several skirmishes with him returned to the Space Colony ARK, where he discovered that Rouge was in fact a G.U.N. spy under orders from the President to learn more about the Ultimate Life Form.

Sonic and his friends boarded the Space Colony ARK to stop Eggman's plan, only to find Shadow in the way. Sonic nearly was killed when he was sent to space in an exploding pod, but was able to escape using Chaos Control, a technique which Shadow had accidently taught him during their first encounter.

Sonic and Shadow fought once again, only for Shadow to get defeated. While Sonic continued searching for Eggman, Amy Rose asked Shadow to help them save the world, and asked him to forgive the humans for whatever they did to him. Shadow instantly remembered Maria's dying words, and vowed that he would protect the world she loved enough to die for.

Shadow met up with Sonic just as a monster appeared. This monster, which was in fact the Ultimate Life Form Prototype, fused itself with the outside of the ARK, pulling it by hand toward the Earth as a last-ditch attempt to destroy the planet; fulfilling Professor Robotnik's plan of revenge.

You see, the Professor was enraged at the death of his granddaughter by the hands of G.U.N., and devised a plan to get his revenge. His plan was to use the Chaos Emeralds to set the Space Colony ARK on a crash course with Earth, which would destroy the planet entirely.

Shadow didn't care about the planet, so he was willing to let the Ultimate Life Form Prototype destroy the planet. However, Amy Rose begged Shadow to reconsider, and to give the human race another chance. Shadow immediately remembered Maria's final wish, and vowed to protect the planet.

Shadow distracted the Prototype, which was code-named Bio Lizard, while Sonic and Knuckles used the Master Emerald to deactivate the Chaos Emeralds, making the collision course with Earth halt. However, the Bio Lizard used Chaos Control to fuse itself with the Space Colony ARK, and physically pulled it towards the Earth.

Sonic and Shadow used the Chaos Emeralds to turn Super, and working together, were able to destroy the Bio Lizard, and use Chaos Control to halt the Space Colony's crash course to the Earth. However, Shadow's energy ran out, and he fell to Earth to his apparent death.

However, several months later, Rouge the Bat accidently found Shadow in a life capsule and released him. You see, after Shadow crashed to Earth, Dr. Eggman found him and put him in a life containment unit and ordered E-123 Omega, the last of the E-100 series robots, to guard him.

Rouge released Shadow, who protected her from Omega, who was angrily destroying all of Eggman's robots to avenge being put in the same room as Shadow. Rouge managed to stop Shadow and Omega before they killed each other, and the three eventually became known as Team Dark.

Team Dark helped to defeat Dr. Eggman's newest plan, and protected the world from the evil Metal Overlord. But then a threat came that Shadow had to face alone: The return of the Black Arms.

The Black Arms were a race of aliens that had visited Earth over 50 years ago. Their leader Black Doom had actually helped with the creation of Shadow, giving the black hedgehog some of his DNA. Now, Black Doom wanted the Chaos Emeralds to destroy the planet. Shadow, after dealing with several temptations, and being constantly reminded of his past, killed Black Doom and destroyed the Black Arms completely. Shadow determined to leave the past behind him, and joined G.U.N. as an undercover agent.

Since then, Shadow has worked with G.U.N. to protect the planet from threats such as the sun god Solaris, the demonic Mephiles, the nasty Time Eater, and most recently: The dreaded Lyric.

Shadow has left the past completely behind him, never mentioning the Space Colony, his creation, or Maria. And everyone for the most part seems to have forgotten about it. That is…until a terrible secret was discovered.

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To be continued...

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><p><strong>AN: So there's the prologue. Before you say anything about Sonic Boom not being canon, I FREAKIN' KNOW THAT! But this is kinda combining that adventure with the Modern Sonic era. (No, Sonic Boom character's WON'T be in it! But one of the characters might reference something that happened in Boom).  
><strong>

**And don't go saying that Mephiles and Solaris are the same being. I know that! But for a long time they were separate, so I mentioned them separately. **

**Anything else I need to cover so people don't hate on this!? Good. I thought not. XD**

**But anyway, what secret was the ARK holding that will soon be discovered? We'll have to find out. **


	2. Chapter 1

_**Chapter 1: Back to the ARK**_

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><p><strong>AN: Here's Chapter 1 of The Secret of the ARK everybody! :D**

**I uploaded this one so people don't only have to read Shadow's past history. Ya'll need something fresh. :)**

**But yeah, I had a lot of fun writing this, and I am loving my own work right now!**

**Enjoy the chapter, and please review and tell me what you think. It really helps me to want to continue it. **

**I do not own Sonic the Hedgehog or any of the characters here! They are sole properties of SEGA and Sonic Team.**

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><p>Six months after the battle with the dreaded Lyric, the Earth seemed to be back to normal for the most part. However, in outer space the situation was completely different.<p>

Onboard the Space Colony ARK, there were sounds and vibrations of explosions, and you could see the wreckage of an intense battle that was taking place that very minute. Two individuals sped by through the hallway, with another individual chasing after them.

"Come on!" One of the individuals said as he ran like the wind. "We gotta lose Met-Butt back there!" He was a blue hedgehog wearing nothing but his gloves and shoes. The person he was talking to was a black and red hedgehog who was dressed in the same fashion.

"If you didn't trip over that trash can he wouldn't have found us!" He growled in a deep voice.

The blue hedgehog laughed nervously. "Come on Shads." He said as he turned around and started running backwards, looking at their attacker. "Where's your sense of adventure!?"

"Probably back in the control room." The black hedgehog muttered under his breath as he jerked to the left, narrowly avoiding a missile that was shot from behind.

Sonic sighed as he stopped suddenly. "Shads, keep him busy!" The blue hedgehog curled up in a ball and began to spin in place.

"Got it!" Shadow jumped at the wall and rebounded off, clashing into their attacker, knocking him to the ground.

"Is that all you got!?" Their attacker asked in a deep, metallic voice. He attempted to punch Shadow, but the black hedgehog simply teleported just out of range. He continued to do so as Sonic charged up. "Stop moving you pest!" The robot hissed as it thrust at Shadow yet again, only for Shadow to grab its arm and throw it to the ground.

"You ready yet Faker!?" Shadow asked impatiently. While he slightly enjoyed beating up the blue robotic hedgehog, he was not in the mood to spend his whole day doing so.

"Yep!" Sonic began glowing bright blue as blue orbs began to surround him. "Outta the way!" He shouted as he flung himself at the metal hedgehog at speeds so fast Shadow was forced to face-plant the ground to avoid getting hit. The attack went right through the robot, and flung it through the wall. "Well," Sonic said, standing up and dusting himself off. "That was fun."

Shadow growled as he stood up. "Next time give me a better warning!" He snapped angrily.

Sonic chuckled. "Alright. Now let's get that Chaos Emerald and get out of here."

Shadow nodded, and the two of them sped down the hallway. After a couple of minutes they reached a large room with several containment devices, each of them empty. The room was eerily lighted by a few lights that occasionally flickered.

"Whoa…" Sonic shuddered as the two hedgehogs walked into the room. "This place is kinda spooky."

Shadow shook his head in disapproval as he walked to one of the desks in the far corner of the room. "Let's just find that Chaos Emerald." He said as he opened and closed the different drawers in the desk.

Sonic nodded as he followed suit to another desk. But as he opened a drawer his elbow hit something that sent a surge of pain through his arm. "Youch!" Sonic exclaimed, jumping in surprise.

Shadow looked at Sonic with a strange look. "What is it?"

"Something just shocked me." Sonic said as Shadow sighed. Apparently Shadow was taking this seriously.

Sonic looked at where his elbow was at, and saw a strange button on the side of the desk. _Hmm,_ Sonic thought to himself. _Strange button plus eerily lit room plus me getting zapped…I'm pushing it. _He pushed the button and the entire ARK began to shake violently.

"Sonic!" Shadow shouted angrily, glaring at the blue hedgehog while trying to keep his balance. "What the hell did you just do!?"

"I just pushed a button!" Sonic shouted back over the noise of everything breaking and shaking. After what seemed like forever…which was actually only three minutes…the ARK stopped shaking.

"Whew!" Sonic said, letting go of the chair he had hung to. "That was unexpected!"

Shadow glared angrily at Sonic. "If our mission wasn't dangerous enough from Metal Sonic, you HAD to go around pushing buttons!?"

Sonic shrugged. "Sorry Shads."

Shadow was about to say something when there was a strange noise. Shadow and Sonic both instinctively got into a fighting position. To the two hedgehog's surprise the far wall began shaking, and after a minute moved to the left, revealing a secret passage.

Sonic let out a whistle. "That's interesting!" He walked to the passage and peered inside. "It's dark too!" He said, his voice echoing loudly.

Shadow walked right past Sonic with a flashlight he had brought with him just in case. Sonic followed the black hedgehog into the passage.

"Man," Sonic whistled again. "This place is dark!" His voice echoed several times in the dark, narrow passage.

"Hmm…" Shadow looked around him as the two walked through the passage. On the walls were depictions of what appeared to be a hedgehog fighting a strange creature, but he couldn't identify what it was. Shadow shrugged as he continued walking, and stopped only when Sonic exclaimed behind him.

"Hey Shads!" Sonic exclaimed, getting the black hedgehog's attention. "You should look at this!"

Shadow turned around and walked back to Sonic. "What is it?" He groaned, thinking that Sonic probably saw a rat or something. What he saw surprised even him: There was a large metal door down a hidden hallway.

"Someone certainly had a lot of time on his hands!" Sonic exclaimed, walking to the door and rubbing his hands on it. "This door's solid steel." He knocked on the door and stepped back in surprise. "And it feels like it is several feet thick!"

"Hmph," Shadow grunted as he walked to the door and examined it. It certainly was very strong, and had a strange lock on it. On the door itself there were strange markings.

"Well," Sonic said smiling to Shadow. "Let's go in."

Shadow nodded, and despite the door being incredibly strong, a few well-aimed kicks by the two hedgehogs brought it down. The two walked into the room and looked around in surprise.

The room was very dimly lit, the only light coming from the corner of the room. All across the room were papers sprawled out on the ground, and broken pieces of glass were everywhere.

"Man," Sonic grumbled as he stepped around the glass. "You'd think this place would be cleaned up better." He bent down and picked up a red jewel that was lying in the corner, which was where the light was coming from. "Hey Shads!" He exclaimed, holding up the jewel. "Found the Chaos Emerald! Let's get out of here."

Shadow didn't say anything, but instead looked at the middle of the room with a strange expression. In the middle of the room was a large stasis unit that had apparently been used not long before. Surrounding it was several pieces of glass, which came from the broken unit.

"Shadow?" Sonic asked, walking to Shadow with a concerned expression on his face. "'Sup?"

Shadow turned to Sonic with a strange expression on his face. "I'm ready." He said quickly. "Let's go."

Sonic nodded. "All right." The blue hedgehog walked out of the room as Shadow looked back at the piece of paper that was hanging on the last piece of glass still standing.

"It's impossible…" He muttered to himself. "It simply can't be…"

"Yo Shads!" Sonic called from the other room. "You coming or what?"

Shadow quickly turned around. "Yes." He said. He looked back at the paper and shook his head. He then turned back to the door and walked to Sonic. "You ready?"

Sonic nodded, and the two held their Chaos Emeralds. "Chaos Control!" There was a bright light as the two hedgehogs vanished from the ARK. The room became dark once again, but a strange light flickered above the stasis unit for a split-second, which had five letters written in bold, red letters: M-A-R-I-A.

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To be continued...

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><p><strong>AN: So there you go! Chapter 1 of this new fanfic! :D**

**I had a lot of fun writing in Sonic's and Shadow's personalities. And writing in the scene where Shadow face-planted the ground actually made me laugh out loud. XD**

**So, with this fanfic I am trying to be as descriptive as possible, which is new compared to my older fanfics. I think I'm doing an OK job, but maybe you guys can give me hints?**

**So anyway, since the Space Colony ARK was over 50 years old, it'd make sense that it had secret passages that not even Shadow knew about. And what about those drawings on the wall? Are they a foreshadowing of some sort? Hmm...**

**And I'm sorry, but I actually had a chill run down my spine when I did the very last part with Maria's name on the paper. Speaking of which: What does that mean? Why is her name written there of all places? You'll have to wait to find out. XD**

**So that's just about it. Thank you all for reading this chapter. Please review and tell me what you think, and I will update soon. Peace out! (Or should I have said Chaos Control?)**


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